HEADER HYDROLASE 08-JUL-16 5KSC
TITLE E166A/R274N/R276N TOHO-1 BETA-LACTAMASE AZTREONAM ACYL-ENZYME
TITLE 2 INTERMEDIATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-LACTAMASE TOHO-1;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.5.2.6;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: AZTREONAM
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: BLA;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BETA-LACTAMASE, AZTREONAM, ACYL-INTERMEDIATE, HYDROLASE
EXPDTA NEUTRON DIFFRACTION
AUTHOR V.G.VANDAVASI,P.S.LANGAN,K.WEISS,J.M.PARKS,J.B.COOPER,S.L.GINELL,
AUTHOR 2 L.COATES
REVDAT 6 09-OCT-24 5KSC 1 REMARK
REVDAT 5 04-DEC-19 5KSC 1 REMARK
REVDAT 4 06-JUN-18 5KSC 1 REMARK
REVDAT 3 20-SEP-17 5KSC 1 REMARK
REVDAT 2 11-JAN-17 5KSC 1 JRNL
REVDAT 1 09-NOV-16 5KSC 0
JRNL AUTH V.G.VANDAVASI,P.S.LANGAN,K.L.WEISS,J.M.PARKS,J.B.COOPER,
JRNL AUTH 2 S.L.GINELL,L.COATES
JRNL TITL ACTIVE-SITE PROTONATION STATES IN AN ACYL-ENZYME
JRNL TITL 2 INTERMEDIATE OF A CLASS A BETA-LACTAMASE WITH A MONOBACTAM
JRNL TITL 3 SUBSTRATE.
JRNL REF ANTIMICROB. AGENTS V. 61 2017
JRNL REF 2 CHEMOTHER.
JRNL REFN ESSN 1098-6596
JRNL PMID 27795378
JRNL DOI 10.1128/AAC.01636-16
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELX SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 72.1
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.280
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1966
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 29
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2011.8
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2024.0
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL
REMARK 3 NUMBER OF RESTRAINTS : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 ANGLE DISTANCES (A) : NULL
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5KSC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-16.
REMARK 100 THE DEPOSITION ID IS D_1000222670.
REMARK 230
REMARK 230 EXPERIMENTAL DETAILS
REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION
REMARK 230 DATE OF DATA COLLECTION : 03-MAR-15
REMARK 230 TEMPERATURE (KELVIN) : 293.0
REMARK 230 PH : 6.10
REMARK 230 NUMBER OF CRYSTALS USED : 1
REMARK 230
REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR
REMARK 230 BEAMLINE : MANDI
REMARK 230 WAVELENGTH OR RANGE (A) : 2-4
REMARK 230 MONOCHROMATOR : NULL
REMARK 230 OPTICS : NULL
REMARK 230
REMARK 230 DETECTOR TYPE : AREA DETECTOR
REMARK 230 DETECTOR MANUFACTURER : ORNL ANGER CAMERA
REMARK 230 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 230 DATA SCALING SOFTWARE : NULL
REMARK 230
REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 13173
REMARK 230 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 230 RESOLUTION RANGE LOW (A) : 14.730
REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 230
REMARK 230 OVERALL.
REMARK 230 COMPLETENESS FOR RANGE (%) : 71.5
REMARK 230 DATA REDUNDANCY : 3.100
REMARK 230 R MERGE (I) : 0.16000
REMARK 230 R SYM (I) : NULL
REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 10.1000
REMARK 230
REMARK 230 IN THE HIGHEST RESOLUTION SHELL.
REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17
REMARK 230 COMPLETENESS FOR SHELL (%) : 50.1
REMARK 230 DATA REDUNDANCY IN SHELL : 2.00
REMARK 230 R MERGE FOR SHELL (I) : 0.26000
REMARK 230 R SYM FOR SHELL (I) : NULL
REMARK 230 <I/SIGMA(I)> FOR SHELL : 4.200
REMARK 230
REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 230 SOFTWARE USED : SHELX
REMARK 230 STARTING MODEL: NULL
REMARK 230
REMARK 230 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MICROLITERS OF A 10 MG/ML PROTEIN
REMARK 280 CONCENTRATION IN A SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE
REMARK 280 AND 0.1 M SODIUM CITRATE (PH 6.1) PREPARED IN D2O., BATCH MODE,
REMARK 280 TEMPERATURE 293.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.06200
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.03100
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.03100
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 66.06200
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ASN A 27 CG OD1 ND2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O ASP A 100 D2 DOD A 404 1.45
REMARK 500 O PRO A 173 D2 DOD A 410 1.57
REMARK 500 O GLY A 216 D2 DOD A 405 1.58
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 CYS A 68 -130.05 57.22
REMARK 500 VAL A 102 -145.06 -124.49
REMARK 500 ASN A 105 75.89 -166.05
REMARK 500 SER A 219 -116.27 -85.50
REMARK 500 ASN A 252 29.62 -142.26
REMARK 500 LYS A 268 47.49 -90.55
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue AZR A 301
DBREF 5KSC A 27 287 UNP Q47066 BLT1_ECOLX 31 291
SEQADV 5KSC ALA A 165 UNP Q47066 GLU 169 ENGINEERED MUTATION
SEQADV 5KSC ASN A 271 UNP Q47066 ARG 275 ENGINEERED MUTATION
SEQADV 5KSC ASN A 273 UNP Q47066 ARG 277 ENGINEERED MUTATION
SEQRES 1 A 261 ASN SER VAL GLN GLN GLN LEU GLU ALA LEU GLU LYS SER
SEQRES 2 A 261 SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASN THR ALA
SEQRES 3 A 261 ASP ASN SER GLN ILE LEU TYR ARG ALA ASP GLU ARG PHE
SEQRES 4 A 261 ALA MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA
SEQRES 5 A 261 VAL LEU LYS GLN SER GLU SER ASP LYS HIS LEU LEU ASN
SEQRES 6 A 261 GLN ARG VAL GLU ILE LYS LYS SER ASP LEU VAL ASN TYR
SEQRES 7 A 261 ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET THR
SEQRES 8 A 261 LEU ALA GLU LEU GLY ALA ALA ALA LEU GLN TYR SER ASP
SEQRES 9 A 261 ASN THR ALA MET ASN LYS LEU ILE ALA HIS LEU GLY GLY
SEQRES 10 A 261 PRO ASP LYS VAL THR ALA PHE ALA ARG SER LEU GLY ASP
SEQRES 11 A 261 GLU THR PHE ARG LEU ASP ARG THR ALA PRO THR LEU ASN
SEQRES 12 A 261 THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR PRO
SEQRES 13 A 261 LEU ALA MET ALA GLN THR LEU LYS ASN LEU THR LEU GLY
SEQRES 14 A 261 LYS ALA LEU ALA GLU THR GLN ARG ALA GLN LEU VAL THR
SEQRES 15 A 261 TRP LEU LYS GLY ASN THR THR GLY SER ALA SER ILE ARG
SEQRES 16 A 261 ALA GLY LEU PRO LYS SER TRP VAL VAL GLY ASP LYS THR
SEQRES 17 A 261 GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA VAL
SEQRES 18 A 261 ILE TRP PRO GLU ASN HIS ALA PRO LEU VAL LEU VAL THR
SEQRES 19 A 261 TYR PHE THR GLN PRO GLU GLN LYS ALA GLU ASN ARG ASN
SEQRES 20 A 261 ASP ILE LEU ALA ALA ALA ALA LYS ILE VAL THR HIS GLY
SEQRES 21 A 261 PHE
HET AZR A 301 28
HETNAM AZR 2-({[(1Z)-1-(2-AMINO-1,3-THIAZOL-4-YL)-2-OXO-2-{[(2S,
HETNAM 2 AZR 3S)-1-OXO-3-(SULFOAMINO)BUTAN-2-
HETNAM 3 AZR YL]AMINO}ETHYLIDENE]AMINO}OXY)-2-METHYLPROPANOIC ACID
HETSYN AZR AZTREONAM, OPEN FORM
FORMUL 2 AZR C13 H19 N5 O8 S2
FORMUL 3 DOD *29(D2 O)
HELIX 1 AA1 SER A 28 GLY A 41 1 14
HELIX 2 AA2 CYS A 68 THR A 70 5 3
HELIX 3 AA3 SER A 71 GLU A 84 1 14
HELIX 4 AA4 LYS A 97 LEU A 101 5 5
HELIX 5 AA5 ILE A 107 VAL A 112 5 6
HELIX 6 AA6 THR A 117 TYR A 128 1 12
HELIX 7 AA7 ASP A 130 GLY A 142 1 13
HELIX 8 AA8 GLY A 143 LEU A 154 1 12
HELIX 9 AA9 PRO A 166 THR A 170 5 5
HELIX 10 AB1 THR A 181 LEU A 194 1 14
HELIX 11 AB2 ALA A 199 GLY A 212 1 14
HELIX 12 AB3 ILE A 220 LEU A 224 5 5
HELIX 13 AB4 ARG A 272 THR A 284 1 13
SHEET 1 AA1 5 GLN A 56 TYR A 59 0
SHEET 2 AA1 5 ARG A 43 ASN A 50 -1 N VAL A 46 O TYR A 59
SHEET 3 AA1 5 LEU A 256 THR A 263 -1 O THR A 263 N ARG A 43
SHEET 4 AA1 5 THR A 242 TRP A 249 -1 N ILE A 248 O LEU A 256
SHEET 5 AA1 5 VAL A 229 SER A 236 -1 N GLY A 235 O ASN A 243
SHEET 1 AA2 2 PHE A 65 ALA A 66 0
SHEET 2 AA2 2 THR A 179 THR A 180 -1 O THR A 180 N PHE A 65
SHEET 1 AA3 2 GLU A 95 ILE A 96 0
SHEET 2 AA3 2 GLY A 114 THR A 115 -1 O GLY A 114 N ILE A 96
LINK OG SER A 69 C20 AZR A 301 1555 1555 1.35
CISPEP 1 ALA A 165 PRO A 166 0 -1.72
SITE 1 AC1 13 CYS A 68 SER A 69 ASN A 103 TYR A 104
SITE 2 AC1 13 SER A 129 ASN A 131 PRO A 166 ASN A 169
SITE 3 AC1 13 LYS A 233 THR A 234 GLY A 235 SER A 236
SITE 4 AC1 13 ASP A 238
CRYST1 73.296 73.296 99.093 90.00 90.00 120.00 P 32 2 1 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013643 0.007877 0.000000 0.00000
SCALE2 0.000000 0.015754 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010092 0.00000